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PubMed1998

[A database for thyroid diseases: evaluation with special reference to potential consequences of a nuclear power plant accident].

The concept of a thyroid disease register based on a relational database system with a structured query language (SQL) is reported. More than 5000 examination findings of benign and malignant thyroid disorders have been recorded so far, covering the period from 1986 to 1996. For epidemiological studies these population-based thyroid diseases data can be allocated to a digital data map by means of the five-digit German postal code. When evaluating the data with regard to the function of the thyroid gland as an indicator of preceding nuclear power plant disasters and fallout, we found neither indicators of an increased incidence of thyroid carcinoma as an aftermath of the Chernobyl disaster nor the occurrence of clusters. The data were supplemented by the results of a survey among all Schleswig-Holstein pathologists involved in the diagnosis of thyroid diseases. Data on childhood carcinoma of the thyroid were also provided by the Childhood Tumor Register of the Institute of Pathology, University of Kiel, and by the Childhood Cancer Register of the University of Mainz.

Databases, Factual↗
PubMed2002

'Human' insulin versus animal insulin in people with diabetes mellitus.

BACKGROUND: Human insulin was introduced for the routine treatment of diabetes mellitus in the early 1980s without adequate comparison of efficacy to animal insulin preparations. First reports of altered hypoglycaemia awareness after transfer to human insulin made physicians and especially patients uncertain about potential adverse effects of human insulin. OBJECTIVES: To assess the effects of different insulin species by evaluating their efficacy (in particular glycaemic control) and adverse effects profile (mainly hypoglycaemia). SEARCH STRATEGY: A highly sensitive search for randomised controlled trials combined with key terms for identifying studies on human versus animal insulin was performed using the Cochrane Library (issue 2, 2002), Medline (1966 to May, 2002) and Embase (1974 to February, 2002). We also searched reference lists and databases of ongoing trials. Date of latest search: May 2002. SELECTION CRITERIA: We included randomised controlled clinical trials with diabetic patients of all ages that compared human to animal (for the most part purified porcine) insulin. Trial duration had to be at least one month in order to achieve reliable results on the main outcome parameter glycated haemoglobin. DATA COLLECTION AND ANALYSIS: Trial selection as well as evaluation of study quality was performed by two independent reviewers. The quality of reporting of each trial was assessed according to a modification of the quality criteria as specified by Schulz and by Jadad. MAIN RESULTS: Altogether 2156 participants took part in the 45 randomised controlled studies that were discovered through extensive search efforts. Though many studies were of a randomised, double-blind design, most studies were of poor methodological quality. Purified porcine and semi-synthetic insulin were most often investigated. No significant differences in metabolic control or hypoglycaemic episodes between various insulin species could be elucidated. Insulin dose and insulin antibodies did not show relevant dissimilarities. REVIEWER'S CONCLUSIONS: A comparison of the effects of human and animal insulin as well as of the adverse reaction profile did not show clinically relevant differences. Many patient-oriented outcomes like health-related quality of life or diabetes complications and mortality were never investigated in high-quality randomised clinical trials. The story of the introduction of human might be repeated by contemporary launching campaigns to introduce pharmaceutical and technological innovations that are not backed up by sufficient proof of their advantages and safety.

Animals↗
PubMed1996

Searching for information on toxicological data of chemical substances in selected bibliographic databases--selection of essential databases for toxicological researches.

By using information from printed and online database guides, 18 online bibliographic databases (BD), which cover literature on toxicology were selected from 5 hosts. A search for literature containing information on three selected chemicals was carried out with each of the databases, and the number of documents relevant to toxicology found in them was compared by computer-assisted analysis. Some databases yielded very little information pertinent to toxicology, while others provided a considerable amount. In addition, the databases contained numerous duplicates (references common to more than one database). Most of the relevant documents could be obtained using only 8 of the 18 BDs selected. These databases are: Biosis Previews (BIOSIS), Chemical Abstracts (CA), Chemical Safety Newsbase (CSNB), Excerpta Medica (EMBASE), National Institute for Occupational Safety and Health (NIOSH), Scisearch, Toxicology Information Online (TOXLINE) and the former Toxicology Literature (TOXLIT).

Databases, Bibliographic↗
PubMed2000

The RESID database of protein structure modifications: 2000 update.

The RESID Database contains supplemental information on post-translational modifications for the standardized annotations appearing in the PIR-International Protein Sequence Database. The RESID Database includes: systematic and frequently observed alternate names, Chemical s Service registry numbers, atomic formulas and weights, enzyme activities, indicators for N-terminal, C-terminal or peptide chain cross-link modifications, keywords, literature citations with database cross-references, structural diagrams and molecular models. Since 1995 updates of the RESID Database have appeared as often as weekly, and full releases appear quarterly. The database is freely accessible through the PIR Web site http://pir.georgetown.edu/pirwww/dbinfo/resid.html and by FTP.

Databases, Factual↗
PubMed2006

Comparison of meat composition from offspring of cloned and conventionally produced boars.

This study compares the meat composition of the offspring from boars produced by somatic cell nuclear transfer (n=4) to that of the offspring from conventionally produced boars (n=3). In total, 89 commercial gilts were artificially inseminated and 61 progressed to term and farrowed. All of the resulting piglets were housed and raised identically under standard commercial settings and slaughtered upon reaching market weight. Loin samples were taken from each slaughtered animal and shipped offsite for meat composition analysis. In total, loin samples from 404 animals (242 from offspring of clones and 162 from controls) were analyzed for 58 different parameters generating 14,036 and 9396 data points from offspring of clones and the controls, respectively. Values for controls were used to establish a range for each parameter. Ten percent was then added to the maximum and subtracted from the minimum of the control range, and all results within this range were considered clinically irrelevant. Of the 14,036 data points from the offspring of clones, only three points were found outside the clinically irrelevant range, two of which were within the range established by the USDA National Nutrient Database for Standard Reference, Release 18, 2005; website: (www.nal.usda.gov/fnic/foodcomp/search/). The only outlier was the presence of Eicosadienoic acid (C20:2) in one sample which is typically present in minute quantities in pork; no reference data were found regarding this fatty acid in the USDA National Nutrient Database. In conclusion, these data indicated that meat from the offspring of clones was not chemically different than meat from controls and therefore supported the case for the safety of meat from the offspring of clones.

Animal Husbandry↗
PubMed2001

The RESID Database of protein structure modifications and the NRL-3D Sequence-Structure Database.

The RESID Database is a comprehensive collection of annotations and structures for protein post-translational modifications including N-terminal, C-terminal and peptide chain cross-link modifications. The RESID Database includes systematic and frequently observed alternate names, Chemical Abstracts Service registry numbers, atomic formulas and weights, enzyme activities, taxonomic range, keywords, literature citations with database cross-references, structural diagrams and molecular models. The NRL-3D Sequence-Structure Database is derived from the three-dimensional structure of proteins deposited with the Research Collaboratory for Structural Bioinformatics Protein Data Bank. The NRL-3D Database includes standardized and frequently observed alternate names, sources, keywords, literature citations, experimental conditions and searchable sequences from model coordinates. These databases are freely accessible through the National Cancer Institute-Frederick Advanced Biomedical Computing Center at these web sites: http://www. ncifcrf.gov/RESID, http://www.ncifcrf.gov/NRL-3D; or at these National Biomedical Research Foundation Protein Information Resource web sites: http://pir.georgetown.edu/pirwww/dbinfo/resid .html, http://pir.georgetown.edu/pirwww/dbinfo/nrl3d .html

Amino Acids↗
PubMed1996

Selecting a database for literature searches in nursing: MEDLINE or CINAHL?

This study compares the usefulness of the MEDLINE and CINAHL databases for students on post-registration nursing courses. We searched for nine topics, using title words only. Identical searches of the two databases retrieved 1162 references, of which 88% were in MEDLINE, 33% in CINAHL and 20% in both sources. The relevance of the references was assessed by student reviewers. The positive predictive value of CINAHL (70%) was higher than that of MEDLINE (54%), but MEDLINE produced more than twice as many relevant references as CINAHL. The sensitivity of MEDLINE was 85% (95% CI 82-88%), and that of CINAHL was 41% (95% CI 37-45%). To assess the ease of obtaining the references, we developed an index of accessibility, based on the holdings of a number of Irish and British libraries. Overall, 47% of relevant references were available in the students' own library, and 64% could be obtained within 48 hours. There was no difference between the two databases overall, but when two topics relating specifically to the organization of nursing were excluded, references found in MEDLINE were significantly more accessible. We recommend that MEDLINE should be regarded as the first choice of bibliographic database for any subject other than one related strictly to the organization of nursing.

Choice Behavior↗
PubMed2004

The Eukaryotic Promoter Database EPD: the impact of in silico primer extension.

The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, experimentally defined by a transcription start site (TSS). There may be multiple promoter entries for a single gene. The underlying experimental evidence comes from journal articles and, starting from release 73, from 5' ESTs of full-length cDNA clones used for so-called in silico primer extension. Access to promoter sequences is provided by pointers to TSS positions in nucleotide sequence entries. The annotation part of an EPD entry includes a description of the type and source of the initiation site mapping data, links to other biological databases and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. Web-based interfaces have been developed that enable the user to view EPD entries in different formats, to select and extract promoter sequences according to a variety of criteria and to navigate to related databases exploiting different cross-references. Tools for analysing sequence motifs around TSSs defined in EPD are provided by the signal search analysis server. EPD can be accessed at http://www.epd. isb-sib.ch.

Animals↗
PubMed1995

Conditional reference charts to assess weight gain in British infants.

Growth monitoring in infancy is a useful tool for detecting growth disorders and failure to thrive. However, current weight charts do not monitor growth as such, they only identify infants whose weight centile is low and/or falling. A reference of conditional weight gain is described which compares an infant's current weight with that predicted from their previous weight, allowing for the fact that on average, light infants tend to grow faster than heavier infants. The reference, which expresses conditional weight gain as an SD score of centile, is based on the UK 1990 weight reference supplemented with correlation data on 223 infants from the Cambridge Infant Growth Study measured regularly between 4 weeks and 2 years of age. The reference is validated with data on 727 infants from the Newcastle Regional Health Authority database. The conditional reference provides a valid assessment of the weight gain of British infants, over time periods of four or more weeks, throughout the first two years of life.

Female↗
PubMedDate not supplied

Biomechanical approaches applied to the lower and upper limb for the measurement of spasticity: a systematic review of the literature.

PURPOSE: To review and characterise biomechanical approaches for the measurement of spasticity as one component of the upper motor neurone syndrome. METHOD: Systematic literature searches based on defined constructs and a four-step review process of approaches used or described to measure spasticity, its association with function or associated phenomena. Most approaches were limited to individual joints and therefore, to reflect this trend, references were grouped according to which body joint(s) were investigated or whether it addressed a functional activity. For each joint, references were further sub-divided into the types of measurement method described. RESULTS: A database of 335 references was established for the review process. The knee, ankle and elbow joints were the most popular, perhaps reflecting the assumption that they are mono-planar in movement and therefore simpler to assess. Seven measurement methods were identified: five involving passive movement (manual, controlled displacement, controlled torque, gravitational and tendon tap) and two involving active movement (voluntary and functional). Generally, the equipment described was in an experimental stage and there was a lack of information on system properties, such as accuracy or reliability. Patient testing was either by cohort or case studies. The review also conveyed the myriad of interpretations of the concept of spasticity. CONCLUSIONS: Though biomechanical approaches provide quantitative data, the review highlighted several limitations that have prevented them being established as an appropriate method for clinical application to measure spasticity.

Arm↗
PubMed1999

O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins.

O-GLYCBASE is a database of glycoproteins with O-linked glycosylation sites. Entries with at least one experimentally verified O-glycosylation site have been compiled from protein sequence databases and literature. Each entry contains information about the glycan involved, the species, sequence, a literature reference and http-linked cross-references to other databases. Version 4.0 contains 179 protein entries, an approximate 15% increase over the last version. Sequence logos representing the acceptor specificity patterns for GalNAc, GlcNAc, mannosyl and xylosyl transferases are shown. The O-GLYCBASE database is available through the WWW at http://www.cbs.dtu.dk/databases/OGLYCBASE/

Acetylgalactosamine↗
PubMed2006

Incomplete pediatric reference intervals for the management of patients with inborn errors of metabolism.

OBJECTIVES: To evaluate the status of pediatric reference intervals for several biomarkers of inborn errors of metabolism (IEM). INTRODUCTION: There are several biomarkers that are used in many laboratories that specialize in biochemical genetics. Among them, there are acylcarnitines, total carnitine, amino acids, essential fatty acids, phytanic acid and very long chain fatty acids. These tests are key to exclusion or inclusion of an IEM, therefore appropriate age-related references intervals are crucial. A detailed review of each selected analyte is given. RESULTS: Published reference intervals do not always address the dependency of age, gender, or ethnic background; they are not established for newer laboratory methodologies and are derived from a limited number of healthy controls for most markers. CONCLUSIONS: To address the gap in pediatric reference intervals, the Canadian research project (CALIPER database) will establish comprehensive reference intervals for acylcarnitines, total carnitine, amino acids, essential fatty acids, phytanic acid, and very long chain fatty acids. All the tests will be limited to whole blood, plasma and serum samples.

Biomarkers↗
PubMed1999

Mapping the literature of perfusion.

Perfusionists select and operate the equipment necessary for monitoring, supporting, or temporarily replacing the patient's circulatory or respiratory function. There are over 3,000 perfusionists working in U.S. hospitals, medical and perfusionist groups, and as independent contractors. The purpose of this study was to identify the core literature of perfusion and to determine which major databases provide the most thorough access to this literature. This paper is part of the Medical Library Association Nursing and Allied Health Resource Section's project to map the literature of the allied health professions. It uses a bibliometric methodology to identify core journals. A group of forty-three journals was determined to make up the core journal literature of perfusion. MEDLINE provided the best overall indexing coverage for these journals, but librarians and perfusionists will wish to supplement its use with the Cumulative Index to Nursing and Allied Health Literature in order to access the journals written primarily for perfusionists. The study results can guide purchasing and database searching decisions of collection development and reference librarians, encourage the database producer to increase coverage of titles that are unindexed or underindexed, and advise perfusionists of the best access to their core literature.

Abstracting and Indexing↗
PubMed2005

Dasty and UniProt DAS: a perfect pair for protein feature visualization.

In this study, we present two freely available and complementary Distributed Annotation System (DAS) resources: a DAS reference server that provides up-to-date sequence and annotation from UniProt, with additional feature links and database cross-references from InterPro and a DAS client implemented using Java and Macromedia Flash that is optimized for the display of protein features.

Algorithms↗
PubMed1982

A personal reference retrieval system for medium sized computers allowing automatic data entry from ONLINE databases.

A series of programs has been developed for the storage and retrieval of bibliographic references, which allow automatic cross-referencing of the stored entries. Reference retrieval becomes successively faster as more searches are performed and references are automatically sub-grouped under indexed terms allow complete sub-sets to be scanned independently. The indexing allows complete sub-collections of references to be printed, e.g. for a review, with no further searching requirements. This style of retrieval is conceptually similar to card systems in use by many scientists and should enable a rapid familiarization with the retrieval system. The editing features of the programs provide for the direct collection of references from large ONLINE databases (e.g. MEDLINE) and the automatic entering of the references into the personal data collection. The programs provide reliable storage of references for individual scientists, so that their collections from library databases, or from manual input may be updated and searched quickly.

Abstracting and Indexing↗
PubMed2005

Rice proteome database: a step toward functional analysis of the rice genome.

The technique of proteome analysis using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) has the power to monitor global changes that occur in the protein complement of tissues and subcellular compartments. In this study, the proteins of rice were cataloged, a rice proteome database was constructed, and a functional characterization of some of the identified proteins was undertaken. Proteins extracted from various tissues and subcellular compartments in rice were separated by 2D-PAGE and an image analyzer was used to construct a display of the proteins. The Rice Proteome Database contains 23 reference maps based on 2D-PAGE of proteins from various rice tissues and subcellular compartments. These reference maps comprise 13129 identified proteins, and the amino acid sequences of 5092 proteins are entered in the database. Major proteins involved in growth or stress responses were identified using the proteome approach. Some of these proteins, including a beta-tubulin, calreticulin, and ribulose-1,5-bisphosphate carboxylase/oxygenase activase in rice, have unexpected functions. The information obtained from the Rice Proteome Database will aid in cloning the genes for and predicting the function of unknown proteins.

Calreticulin↗
PubMed2003

Predicting ADME properties and side effects: the BioPrint approach.

Computational methods are increasingly used to streamline and enhance the lead discovery and optimization process. However, accurate prediction of absorption, distribution, metabolism and excretion (ADME) and adverse drug reactions (ADR) is often difficult, due to the complexity of underlying physiological mechanisms. Modeling approaches have been hampered by the lack of large, robust and standardized training datasets. In an extensive effort to build such a dataset, the BioPrint database was constructed by systematic profiling of nearly all drugs available on the market, as well as numerous reference compounds. The database is composed of several large datasets: compound structures and molecular descriptors, in vitro ADME and pharmacology profiles, and complementary clinical data including therapeutic use information, pharmacokinetics profiles and ADR profiles. These data have allowed the development of computational tools designed to integrate a program of computational chemistry into library design and lead development. Models based on chemical structure are strengthened by in vitro results that can be used as additional compound descriptors to predict complex in vivo endpoints. The BioPrint pharmacoinformatics platform represents a systematic effort to accelerate the process of drug discovery, improve quantitative structure-activity relationships and develop in vitro/in vivo associations. In this review, we will discuss the importance of training set size and diversity in model development, the implementation of linear and neighborhood modeling approaches, and the use of in silico methods to predict potential clinical liabilities.

Animals↗